NC_000006.11:g.(?_42162409)_(44154249_?)del AND not provided

This record was updated by the submitter. Please see the current version.

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Dec 3, 2021
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

Somatic classification of clinical impact:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Somatic classification of oncogenicity:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Record status:: current
Accession:: RCV003107587.4

Allele description

NC_000006.11:g.(?_42162409)_(44154249_?)del

Genes:

DNPH1:2'-deoxynucleoside 5'-phosphate N-hydrolase 1 [Gene - OMIM - HGNC]
ABCC10:ATP binding cassette subfamily C member 10 [Gene - OMIM - HGNC]
BICRAL:BICRA like chromatin remodeling complex associated protein [Gene - OMIM - HGNC]
POLH:DNA polymerase eta [Gene - OMIM - HGNC]
GTPBP2:GTP binding protein 2 [Gene - OMIM - HGNC]
MAD2L1BP:MAD2L1 binding protein [Gene - OMIM - HGNC]
POLR1C:RNA polymerase I and III subunit C [Gene - OMIM - HGNC]
YIPF3:Yip1 domain family member 3 [Gene - OMIM - HGNC]
CAPN11:calpain 11 [Gene - OMIM - HGNC]
CNPY3:canopy FGF signaling regulator 3 [Gene - OMIM - HGNC]
C6orf226:chromosome 6 open reading frame 226 [Gene - HGNC]
CUL7:cullin 7 [Gene - OMIM - HGNC]
CUL9:cullin 9 [Gene - OMIM - HGNC]
CRIP3:cysteine rich protein 3 [Gene - HGNC]
DLK2:delta like non-canonical Notch ligand 2 [Gene - HGNC]
XPO5:exportin 5 [Gene - OMIM - HGNC]
GNMT:glycine N-methyltransferase [Gene - OMIM - HGNC]
GUCA1B:guanylate cyclase activator 1B [Gene - OMIM - HGNC]
KLHDC3:kelch domain containing 3 [Gene - OMIM - HGNC]
KLC4:kinesin light chain 4 [Gene - OMIM - HGNC]
LRRC73:leucine rich repeat containing 73 [Gene - HGNC]
LINC03040:long intergenic non-protein coding RNA 3040 [Gene - HGNC]
MEA1:male-enhanced antigen 1 [Gene - OMIM - HGNC]
MRPL14:mitochondrial ribosomal protein L14 [Gene - OMIM - HGNC]
MRPL2:mitochondrial ribosomal protein L2 [Gene - OMIM - HGNC]
MRPS10:mitochondrial ribosomal protein S10 [Gene - OMIM - HGNC]
MRPS18A:mitochondrial ribosomal protein S18A [Gene - OMIM - HGNC]
PRPH2:peripherin 2 [Gene - OMIM - HGNC]
PEX6:peroxisomal biogenesis factor 6 [Gene - OMIM - HGNC]
PTCRA:pre T cell antigen receptor alpha [Gene - OMIM - HGNC]
PPP2R5D:protein phosphatase 2 regulatory subunit B'delta [Gene - OMIM - HGNC]
PTK7:protein tyrosine kinase 7 (inactive) [Gene - OMIM - HGNC]
RSPH9:radial spoke head component 9 [Gene - OMIM - HGNC]
RRP36:ribosomal RNA processing 36 [Gene - OMIM - HGNC]
RPL7L1:ribosomal protein L7 like 1 [Gene - OMIM - HGNC]
SRF:serum response factor [Gene - OMIM - HGNC]
SLC22A7:solute carrier family 22 member 7 [Gene - OMIM - HGNC]
TTBK1:tau tubulin kinase 1 [Gene - OMIM - HGNC]
TJAP1:tight junction associated protein 1 [Gene - OMIM - HGNC]
TRERF1:transcriptional regulating factor 1 [Gene - OMIM - HGNC]
TMEM63B:transmembrane protein 63B [Gene - OMIM - HGNC]
TBCC:tubulin folding cofactor C [Gene - OMIM - HGNC]
UBR2:ubiquitin protein ligase E3 component n-recognin 2 [Gene - OMIM - HGNC]
VEGFA:vascular endothelial growth factor A [Gene - OMIM - HGNC]
ZNF318:zinc finger protein 318 [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

6p21.1

Genomic location:

Chr6: 42162409 - 44154249 (on Assembly GRCh37)

Preferred name:

NC_000006.11:g.(?_42162409)_(44154249_?)del

HGVS:

NC_000006.11:g.(?_42162409)_(44154249_?)del

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

Clear Turn Off Turn On

Mus musculus phosphoribosyl pyrophosphate synthetase-associated protein 2, mRNA ...
Mus musculus phosphoribosyl pyrophosphate synthetase-associated protein 2, mRNA (cDNA clone MGC:118451 IMAGE:6512229), complete cds
gi|76780246|gb|BC106185.1|

Nucleotide
Mus musculus adult male corpora quadrigemina cDNA, RIKEN full-length enriched li...
Mus musculus adult male corpora quadrigemina cDNA, RIKEN full-length enriched library, clone:B230333C16 product:hypothetical protein, full insert sequence
gi|26337766|dbj|AK046006.1|

Nucleotide
Mus musculus membrane magnesium transporter 2, mRNA (cDNA clone MGC:106107 IMAGE...
Mus musculus membrane magnesium transporter 2, mRNA (cDNA clone MGC:106107 IMAGE:5025927), complete cds
gi|66794504|gb|BC096583.1|

Nucleotide
glyceraldehyde 3-phosphate dehydrogenase, partial [Almutaster pauciflorus]
glyceraldehyde 3-phosphate dehydrogenase, partial [Almutaster pauciflorus]
gi|197700621|gb|ACH72246.1|

Protein

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

Help

Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003794575	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Dec 3, 2021)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003794575

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Dec 3, 2021)

germline

clinical testing

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Invitae, SCV003794575.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

Description

In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. This variant has not been reported in the literature in individuals affected with GUCA1B-related conditions. This sequence change is a complex rearrangement involving exon 1 of the GUCA1B gene. Although the exact nature of the event is unknown, it likely involves partial deletion and/or inversion of this exon.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Sep 1, 2024

ClinVar

Relating variation to medicine